Compiling error the Python interface

hi!

i have some problem, i read user guide, and test compile with gcc, for example cylinder2d.

good! very good!

but now i tried Compiling the Python interface.

now i using ubuntu 11.10, and ram 8gb

of course, export PALABOS_ROOT and
i installed that
g++
python
python-dev
mpi-default-bin,
mpi-default-dev
mpich2
Swig
NumPy
SciPy
Matplotlib
Mpi4py
mayavi2

this is compile error message


oilsok@ubuntu:~/PALABOS/pythonic/src$ make
cd compilePalabos; make
make[1]: Entering directory `/home/oilsok/PALABOS/pythonic/src/compilePalabos'
python /home/oilsok/PALABOS/pythonic/src/compilePalabos/../../..//scons/scons.py -j 4 -f /home/oilsok/PALABOS/pythonic/src/compilePalabos/../../..//SConstruct palabosRoot=/home/oilsok/PALABOS/pythonic/src/compilePalabos/../../../ projectFiles="dummyMain.cpp" precompiled=true optimize=true debug=false profile=false MPIparallel=true SMPparallel=false usePOSIX=true useCVMLCPP=false serialCXX=g++ parallelCXX=mpicxx dynamicLibrary=true compileFlags="" linkFlags="" optimFlags="-O3" debugFlags="-g" profileFlags="-pg" libraryPaths="" includePaths="" libraries=""
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
scons: `.' is up to date.
scons: done building targets.
make[1]: Leaving directory `/home/oilsok/PALABOS/pythonic/src/compilePalabos'
bash ./preprocess
~/PALABOS/pythonic/src/swig ~/PALABOS/pythonic/src
Swig-file preparation for module core
Swig-file specialization for module int_block
Swig-file specialization for module double_block
Swig-file specialization for module float_block
Swig-file specialization for module double_d2q9
Swig-file specialization for module float_d2q9
Swig-file specialization for module double_d3q19
Swig-file specialization for module float_d3q19
~/PALABOS/pythonic/src
python /home/oilsok/PALABOS//scons/scons.py -j 4 -f /home/oilsok/PALABOS//pythonic/src//SConstruct palabosRoot=/home/oilsok/PALABOS/ pypalRoot=/home/oilsok/PALABOS//pythonic/src/ optimize=true debug=true profile=false MPIparallel=true serialCXX=g++ parallelCXX=mpicxx compileFlags="" optimFlags="-O3" debugFlags="-g" profileFlags="-pg" includePaths="/usr/lib64/python2.4/site-packages/numpy/core/include/" linkFlags=""
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
mpicxx -o precompiled/lattice/d2q9_double/smagorinksyDynamics2D.os -c -O3 -g -DPLB_DEBUG -DPLB_MPI_PARALLEL -DCOMPILE_2D -DFLOAT_T=double -DDESCRIPTOR_2D=D2Q9Descriptor -DNUMBIT_2D=9 -fPIC -I/home/oilsok/PALABOS/src -I/home/oilsok/PALABOS/externalLibraries -I. -I/usr/lib64/python2.4/site-packages/numpy/core/include precompiled/lattice/d2q9_double/smagorinksyDynamics2D.cpp
mpicxx -o precompiled/lattice/d2q9_float/metaStuffWrapper2D.os -c -O3 -g -DPLB_DEBUG -DPLB_MPI_PARALLEL -DCOMPILE_2D -DFLOAT_T=float -DDESCRIPTOR_2D=D2Q9Descriptor -DNUMBIT_2D=9 -fPIC -I/home/oilsok/PALABOS/src -I/home/oilsok/PALABOS/externalLibraries -I. -I/usr/lib64/python2.4/site-packages/numpy/core/include precompiled/lattice/d2q9_float/metaStuffWrapper2D.cpp
mpicxx -o precompiled/lattice/d2q9_float/mrtDynamics.os -c -O3 -g -DPLB_DEBUG -DPLB_MPI_PARALLEL -DCOMPILE_2D -DFLOAT_T=float -DDESCRIPTOR_2D=D2Q9Descriptor -DNUMBIT_2D=9 -fPIC -I/home/oilsok/PALABOS/src -I/home/oilsok/PALABOS/externalLibraries -I. -I/usr/lib64/python2.4/site-packages/numpy/core/include precompiled/lattice/d2q9_float/mrtDynamics.cpp
mpicxx -o precompiled/lattice/d2q9_float/wrappedLocalBoundaryProcessor2D.os -c -O3 -g -DPLB_DEBUG -DPLB_MPI_PARALLEL -DCOMPILE_2D -DFLOAT_T=float -DDESCRIPTOR_2D=D2Q9Descriptor -DNUMBIT_2D=9 -fPIC -I/home/oilsok/PALABOS/src -I/home/oilsok/PALABOS/externalLibraries -I. -I/usr/lib64/python2.4/site-packages/numpy/core/include precompiled/lattice/d2q9_float/wrappedLocalBoundaryProcessor2D.cpp
In file included from precompiled/lattice/d2q9_double/smagorinksyDynamics2D.cpp:31:0:
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:76: error: expected template-name before ‘<’ token
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:76: error: expected ‘{’ before ‘<’ token
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:76: error: expected unqualified-id before ‘<’ token
In file included from precompiled/lattice/d2q9_double/smagorinksyDynamics2D.cpp:32:0:
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.hh:207:59: error: template definition of non-template ‘int plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>::id’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.hh:214:30: error: invalid use of incomplete type ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:7: error: declaration of ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.hh:222:78: error: invalid use of incomplete type ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:7: error: declaration of ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.hh:229:117: error: invalid use of incomplete type ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:7: error: declaration of ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.hh:234:67: error: invalid use of incomplete type ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:7: error: declaration of ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.hh:239:104: error: invalid use of incomplete type ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:7: error: declaration of ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.hh:246:108: error: invalid use of incomplete type ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:7: error: declaration of ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.hh:256:37: error: invalid use of incomplete type ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:7: error: declaration of ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.hh:280:30: error: invalid use of incomplete type ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
/home/oilsok/PALABOS/src/complexDynamics/smagorinskyDynamics.h:94:7: error: declaration of ‘class plb::GuoExternalForceSmagorinskyBGKdynamics<T, Descriptor>’
scons: *** [precompiled/lattice/d2q9_double/smagorinksyDynamics2D.os] Error 1
scons: building terminated because of errors.
make: *** [compilation] error 2


plz help!!

Hi Oilsok,

Thank you very much for this detailed bug report. The bug was fixed, and an updated release (v1.0r1) is online. Please let us know if you still have problems with the Python interface.

Cheers,
Jonas

thx very much!

I have installed the package required,but the bug is :

think@ubuntu:~/palabos-v1.2r0/pythonic/src$ make
cd compilePalabos; make
make[1]: Entering directory /home/think/palabos-v1.2r0/pythonic/src/compilePalabos' python /home/think/palabos-v1.2r0/pythonic/src/compilePalabos/../../..//scons/scons.py -j 2 -f /home/think/palabos-v1.2r0/pythonic/src/compilePalabos/../../..//SConstruct palabosRoot=/home/think/palabos-v1.2r0/pythonic/src/compilePalabos/../../../ projectFiles="dummyMain.cpp" precompiled=true optimize=true debug=false profile=false MPIparallel=true SMPparallel=false usePOSIX=true serialCXX=g++ parallelCXX=mpicxx dynamicLibrary=true compileFlags="-Wl,--no-as-needed, -Wall -Wnon-virtual-dtor " linkFlags="" optimFlags="-O3" debugFlags="-g" profileFlags="-pg" libraryPaths="" includePaths="" libraries="" scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons:.’ is up to date.
scons: done building targets.
make[1]: Leaving directory /home/think/palabos-v1.2r0/pythonic/src/compilePalabos' bash ./preprocess ./preprocess: line 3: pushd: /pythonic/src//swig: No such file or directory Swig-file preparation for module core ./preprocess: line 6: cd: core: No such file or directory ./preprocess: line 10: pre_processed/*.i: No such file or directory ./preprocess: line 9: *.i: No such file or directory ./preprocess: line 14: cd: block: No such file or directory Swig-file specialization for module int_block ./preprocess: line 18: *.i: No such file or directory ./preprocess: line 21: int/*.i: No such file or directory Swig-file specialization for module double_block ./preprocess: line 26: *.i: No such file or directory ./preprocess: line 29: double/*.i: No such file or directory Swig-file specialization for module float_block ./preprocess: line 34: *.i: No such file or directory ./preprocess: line 37: float/*.i: No such file or directory ./preprocess: line 42: cd: blockLattice2d: No such file or directory Swig-file specialization for module double_d2q9 ./preprocess: line 46: *.i: No such file or directory ./preprocess: line 50: double_d2q9/*.i: No such file or directory Swig-file specialization for module float_d2q9 ./preprocess: line 55: *.i: No such file or directory ./preprocess: line 59: float_d2q9/*.i: No such file or directory ./preprocess: line 64: cd: fluid2d: No such file or directory Swig-file specialization for module double_d2q9_fluid ./preprocess: line 72: double_d2q9_fluid/*.i: No such file or directory ./preprocess: line 68: *.i: No such file or directory Swig-file specialization for module float_d2q9_fluid ./preprocess: line 77: *.i: No such file or directory ./preprocess: line 81: float_d2q9_fluid/*.i: No such file or directory ./preprocess: line 86: cd: blockLattice3d: No such file or directory Swig-file specialization for module double_d3q19 ./preprocess: line 94: double_d3q19/*.i: No such file or directory ./preprocess: line 90: *.i: No such file or directory Swig-file specialization for module float_d3q19 ./preprocess: line 99: *.i: No such file or directory ./preprocess: line 103: float_d3q19/*.i: No such file or directory Swig-file specialization for module double_d3q7_ad ./preprocess: line 112: double_d3q7_ad/*.i: No such file or directory ./preprocess: line 108: *.i: No such file or directory Swig-file specialization for module float_d3q7_ad ./preprocess: line 117: *.i: No such file or directory ./preprocess: line 121: float_d3q7_ad/*.i: No such file or directory ./preprocess: line 126: cd: fluid3d: No such file or directory Swig-file specialization for module double_d3q19_fluid ./preprocess: line 130: *.i: No such file or directory ./preprocess: line 134: double_d3q19_fluid/*.i: No such file or directory Swig-file specialization for module float_d3q19_fluid ./preprocess: line 139: *.i: No such file or directory ./preprocess: line 143: float_d3q19_fluid/*.i: No such file or directory ./preprocess: line 148: cd: advectionDiffusion3d: No such file or directory Swig-file specialization for module double_d3q7_advectionDiffusion ./preprocess: line 152: *.i: No such file or directory ./preprocess: line 156: double_d3q7_advectionDiffusion/*.i: No such file or directory Swig-file specialization for module float_d3q7_advectionDiffusion ./preprocess: line 165: float_d3q7_advectionDiffusion/*.i: No such file or directory ./preprocess: line 161: *.i: No such file or directory ./preprocess: line 170: popd: directory stack empty /bin/cp: cannot stat/pythonic/src//precompiled/floatOnly/.cpp’: No such file or directory
/bin/cp: cannot stat /pythonic/src//precompiled/floatOnly/*.cpp': No such file or directory /bin/cp: cannot stat/pythonic/src//precompiled/intOrFloat/
.cpp’: No such file or directory
/bin/cp: cannot stat /pythonic/src//precompiled/intOrFloat/*.cpp': No such file or directory /bin/cp: cannot stat/pythonic/src//precompiled/intOrFloat/.cpp’: No such file or directory
/bin/cp: cannot stat /pythonic/src//precompiled/lattice/*.cpp': No such file or directory /bin/cp: cannot stat/pythonic/src//precompiled/lattice/
.cpp’: No such file or directory
/bin/cp: cannot stat /pythonic/src//precompiled/lattice/*.cpp': No such file or directory /bin/cp: cannot stat/pythonic/src//precompiled/lattice/.cpp’: No such file or directory
/bin/cp: cannot stat /pythonic/src//precompiled/lattice/*.cpp': No such file or directory /bin/cp: cannot stat/pythonic/src//precompiled/lattice/
.cpp’: No such file or directory
/bin/cp: cannot stat /pythonic/src//plbWrapper/block/*.cpp': No such file or directory /bin/cp: cannot stat/pythonic/src//plbWrapper/block/.cpp’: No such file or directory
/bin/cp: cannot stat /pythonic/src//plbWrapper/block/*.cpp': No such file or directory /bin/cp: cannot stat/pythonic/src//plbWrapper/lattice/
.cpp’: No such file or directory
/bin/cp: cannot stat /pythonic/src//plbWrapper/lattice/*.cpp': No such file or directory /bin/cp: cannot stat/pythonic/src//plbWrapper/lattice/.cpp’: No such file or directory
/bin/cp: cannot stat /pythonic/src//plbWrapper/lattice/*.cpp': No such file or directory /bin/cp: cannot stat/pythonic/src//plbWrapper/lattice/
.cpp’: No such file or directory
/bin/cp: cannot stat `/pythonic/src//plbWrapper/lattice/*.cpp’: No such file or directory
make: *** [compilation] Error 1

how should I do with it?

Hello,

I am linux newbie and have an error as well.

PS. Thank you for the music, as the swedes say! Palabos is great!

Lubo


~./pythonics/src$ export PALABOS_ROOT=/home/lap/Work/palabos-v1.2r0/
~./pythonics/src$ make
... (to make it shorter I ommit parts of the messeges) ...
/home/lap/Work/palabos-v1.2r0/src/basicDynamics/isoThermalDynamics.hh:1256:47: note: declarations in dependent base ‘plb::BasicBulkDynamics<double, plb::descriptors::ForcedD2Q9Descriptor>’ are not found by unqualified lookup
/home/lap/Work/palabos-v1.2r0/src/basicDynamics/isoThermalDynamics.hh:1256:47: note: use ‘this->setOmega’ instead
scons: *** [precompiled/lattice/d2q9_double/isoThermalDynamics2D.os] Error 1
scons: building terminated because of errors.
make: *** [compilation] Error 2